Question: ATP reacts with which protein?
Paraphrase: What protein causes a reaction with ATP?
SPARQL (Wikidata):  select distinct ?sbj where { ?sbj wdt:P129 wd:Q80863 . ?sbj wdt:P31 wd:Q8054 } 
Answer: Ryanodine receptor 2, Transient receptor potential cation channel subfamily M member 4, Transient receptor potential cation channel subfamily M member 7, Potassium inwardly rectifying channel, subfamily J, member 11, Transient receptor potential cation channel, subfamily M, member 4, Inositol 1,4,5-trisphosphate receptor type 1, Purinergic receptor P2X 4, G protein-coupled receptor 17, Purinergic receptor P2X 1, Purinergic receptor P2X 3, Purinergic receptor P2Y1, Purinergic receptor P2Y11, Purinergic receptor P2Y13, Pyrimidinergic receptor P2Y4, Purinergic receptor P2Y2, Purinergic receptor P2X 7, Ryanodine receptor 1, Ryanodine receptor 3, Potassium inwardly-rectifying channel, subfamily J, member 8, P2X purinoceptor 4